EpiCompare compares different epigenetic datasets for quality control and benchmarking purposes. The report is divided into three sections:
Total of 6 peak files:
## [1] "File1: active_seacr"
## [1] "File2: active_macs"
## [1] "File3: H3K27me3_seacr"
## [1] "File4: H3K27me3_macs"
## [1] "File5: CnT_seacr"
## [1] "File6: CnT_macs"
Column Description:
PeakN before tidy: Total number of peaks including those blacklisted and those in non-standard chromosomes.
Blacklisted peaks removed (%): Percentage of blacklisted peaks present in the sample. ENCODE blacklist includes regions in the hg19 genome that have anomalous and/or unstructured signals independent of the cell-line or experiment.
Non-standard peaks removed (%): Percentage of peaks identified in non-standard and/or mitochondrial chromosomes. Identified using BRGenomics::tidyChromosomes().
PeakN after tidy: Total number of peaks after filtering blacklisted peaks and those in non-standard chromosomes.
NB: All analyses in EpiCompare are conducted on tidied datasets (i.e. blacklisted peaks and those in non-standard chromosomes removed)
| Sample | PeakN before tidy | Blacklisted peaks removed (%) | Non-standard peaks removed (%) | PeakN after tidy |
|---|---|---|---|---|
| active_seacr | 3211 | 17.80 | 4.390 | 2497 |
| active_macs | 2526 | 23.20 | 7.050 | 1762 |
| H3K27me3_seacr | 107569 | 2.93 | 0.435 | 103953 |
| H3K27me3_macs | 89900 | 2.85 | 0.414 | 86965 |
| CnT_seacr | 6669 | 3.42 | 0.390 | 6415 |
| CnT_macs | 13456 | 3.47 | 0.498 | 12922 |
Metrics on fragments is shown only if Picard summary is provided. See manual for help.
Column Description:
Distribution of peak widths in each sample.
Heatmap of percentage of overlapping peaks between samples. Hover over the heatmap for percentage values.
The plot is shown only if a reference peak file is provided and stat_plot = TRUE. Depending on the format of the reference file, EpiCompare outputs different plots:
ChromHMM annotates and characterises peaks into different chromatin states. The annotation used in EpiCompare were obtained from here. f
ChromHMM annotation of individual samples.
ChromHMM annotation of sample peaks found in reference peaks.
ChromHMM annotation of reference peaks found in sample peaks.
ChromHMM annotation of sample peaks not found in reference peaks.
ChromHMM annotation of reference peaks not found in sample peaks.
EpiCompare uses annotatePeak function in ChIPseeker package to annotate peaks with the nearest gene and genomic region where the peak is located. The peaks are annotated with genes taken from the annotations of human genome hg19 provided by Bioconductor.
EpiCompare performs KEGG pathway and GO enrichment analysis using clusterProfiler. annotatePeak function in ChIPseeker package is first used to assign peaks to nearest genes and biological themes amongst the genes are identified using ontologies (KEGG and GO). The peaks are annotated with genes taken from the annotations of human genome hg19 provided by Bioconductor.